Packages and ports are installed to /usr/local/, as /usr/ different filesystem, this is not the cause of the problem.

See if there's anything that can be removed in /root, this is the home dir for the root user.
Also, when installing a new kernel, the old kernel is moved to /boot/kernel.old, if this directory is present, and the current kernel is working fine, then you can remove this.

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UNIX was not designed to stop you from doing stupid things, because that would also stop you from doing clever things.